The IPI evidence code doc states:
"We recommend making an entry in the "with" column when using this
evidence code; i.e., include an identifier for the "other" protein (or
other macromolecule) involved in the interaction."
From this statement, one could conclude that Gene record IDs are not
allowed.
-Doug
Midori Harris wrote:
> Can someone point me to the offending bit of documentation? The Annotation
> Guide does have this:
>> "Note that a gene ID may be used in the 'with' column for a IPI
> annotation, or for an ISS annotation based on amino acid sequence or
> protein structure similarity, if the database does not have identifiers
> for individual gene products."
>> ... so if there's anyting elsewhere that says otherwise, it needs fixing!
>> (The existing passage can also be reworded to explicitly allow 'for
> whatever reason, you can't tell which protein ID to use'.)
>> thanks,
> m
>> On Tue, 28 Feb 2006, Suzanna Lewis wrote:
>>>> I'm with you on this Karen, but apparently it made it into the
>> documentation somewhere.
>>>> On Feb 28, 2006, at 5:01 PM, Karen Christie wrote:
>>>>>>> I don't believe we've ever implemented a restriction that the ID in the
>>> with column had to be a protein ID for IPI with, because I would have
>>> objected strenously to the suggestion, especially early on when some
>>> SGD
>>> genes didn't even have corresponding protein IDs.
>>>>>> -Karen
>>>>>>>>> On Tue, 28 Feb 2006, Suzanna Lewis wrote:
>>>>>>>>>> BTW, I'm not sure when and where that restriction on the with column
>>>> arose, it seems quite unnecessary.
>>>>>>>> -S
>>>>>>>> On Feb 28, 2006, at 3:43 PM, Doug howe wrote:
>>>>>>>>>>>>> Perhaps this also relates to the relationship between the evidence
>>>>> code and the allowed type of object in the 'with' column. Does it
>>>>> create a computational problem if IPI annotations have both protein
>>>>> and gene IDs in the 'with' column since one is sequence and one is DB
>>>>> identifier? I suppose it isn't all that bad since no matter what you
>>>>> put there, it will have a dbxref associated with it...
>>>>>>>>>> -Doug
>>>>>>>>>> Kimberly Van Auken wrote:
>>>>>>>>>>> Hi Doug--
>>>>>>>>>>>> We have come across this situation here at WormBase and have found
>>>>>> that even though we have
>>>>>> protein IDs corresponding to all confirmed (or even partially
>>>>>> confirmed) transcripts, it is often
>>>>>> difficult, if not impossible, to tell exactly which proteins authors
>>>>>> studied in interaction experiments,
>>>>>> be it two-hybrid assays, co-IPs, etc.
>>>>>>>>>>>> In these cases, we feel that putting the gene ID in the WITH column
>>>>>> is the best compromise.
>>>>>> Doing so still allows users to identify the interacting entities,
>>>>>> but
>>>>>> does not make any potentially
>>>>>> misleading statements about exactly which proteins were involved.
>>>>>>>>>>>> I am also curious to know how other groups handle this. Best,
>>>>>> Kimberly
>>>>>>>>>>>>>>>>>>>>>>>> Doug howe wrote:
>>>>>>>>>>>>>>>>>>> We (curators working from primary literature) often find
>>>>>>> circumstances for IPI annotation where the authors do not provide
>>>>>>> specific information about exactly which protein they are working
>>>>>>> with...though we usually know which gene it came from. So when
>>>>>>> making IPI annotations, where the exact sequence of the protein
>>>>>>> involved is questionable, is it better to put a representative
>>>>>>> protein ID in the "with" field, put the ID of the gene itself in
>>>>>>> the
>>>>>>> with field (is this even valid?), or leave the "with" field empty?
>>>>>>>>>>>>>> How often do other groups actually find that they know the exact
>>>>>>> protein sequence ID of the interacting proteins?
>>>>>>> -Doug
>>>>>>>>>>>>>>>>>>>>>>>>